{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,21]],"date-time":"2026-09-21T22:23:28Z","timestamp":1790029408957,"version":"4.0.1"},"reference-count":226,"publisher":"MDPI AG","issue":"1","license":[{"start":{"date-parts":[[2023,12,28]],"date-time":"2023-12-28T00:00:00Z","timestamp":1703721600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Garnett Passe and Rodney Williams Memorial Foundation","award":["#1182929"],"award-info":[{"award-number":["#1182929"]}]},{"name":"Garnett Passe and Rodney Williams Memorial Foundation","award":["#1181054"],"award-info":[{"award-number":["#1181054"]}]},{"name":"Garnett Passe and Rodney Williams Memorial Foundation","award":["#1170958"],"award-info":[{"award-number":["#1170958"]}]},{"name":"Garnett Passe and Rodney Williams Memorial Foundation","award":["1138604"],"award-info":[{"award-number":["1138604"]}]},{"name":"National Health and Medical Research Council of Australia","award":["#1182929"],"award-info":[{"award-number":["#1182929"]}]},{"name":"National Health and Medical Research Council of Australia","award":["#1181054"],"award-info":[{"award-number":["#1181054"]}]},{"name":"National Health and Medical Research Council of Australia","award":["#1170958"],"award-info":[{"award-number":["#1170958"]}]},{"name":"National Health and Medical Research Council of Australia","award":["1138604"],"award-info":[{"award-number":["1138604"]}]},{"name":"University of British Columbia","award":["#1182929"],"award-info":[{"award-number":["#1182929"]}]},{"name":"University of British Columbia","award":["#1181054"],"award-info":[{"award-number":["#1181054"]}]},{"name":"University of British Columbia","award":["#1170958"],"award-info":[{"award-number":["#1170958"]}]},{"name":"University of British Columbia","award":["1138604"],"award-info":[{"award-number":["1138604"]}]},{"name":"Rebecca L Cooper Foundation","award":["#1182929"],"award-info":[{"award-number":["#1182929"]}]},{"name":"Rebecca L Cooper Foundation","award":["#1181054"],"award-info":[{"award-number":["#1181054"]}]},{"name":"Rebecca L Cooper Foundation","award":["#1170958"],"award-info":[{"award-number":["#1170958"]}]},{"name":"Rebecca L Cooper Foundation","award":["1138604"],"award-info":[{"award-number":["1138604"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["JCM"],"abstract":"<jats:p>Chronic wet cough for longer than 4 weeks is a hallmark of chronic suppurative lung diseases (CSLD), including protracted bacterial bronchitis (PBB), and bronchiectasis in children. Severe lower respiratory infection early in life is a major risk factor of PBB and paediatric bronchiectasis. In these conditions, failure to clear an underlying endobronchial infection is hypothesised to drive ongoing inflammation and progressive tissue damage that culminates in irreversible bronchiectasis. Historically, the microbiology of paediatric chronic wet cough has been defined by culture-based studies focused on the detection and eradication of specific bacterial pathogens. Various \u2018omics technologies now allow for a more nuanced investigation of respiratory pathobiology and are enabling development of endotype-based models of care. Recent years have seen substantial advances in defining respiratory endotypes among adults with CSLD; however, less is understood about diseases affecting children. In this review, we explore the current understanding of the airway microbiome among children with chronic wet cough related to the PBB\u2013bronchiectasis diagnostic continuum. We explore concepts emerging from the gut\u2013lung axis and multi-omic studies that are expected to influence PBB and bronchiectasis endotyping efforts. We also consider how our evolving understanding of the airway microbiome is translating to new approaches in chronic wet cough diagnostics and treatments.<\/jats:p>","DOI":"10.3390\/jcm13010171","type":"journal-article","created":{"date-parts":[[2023,12,28]],"date-time":"2023-12-28T03:30:34Z","timestamp":1703734234000},"page":"171","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":11,"title":["The Respiratory Microbiome in Paediatric Chronic Wet Cough: What Is Known and Future Directions"],"prefix":"10.3390","volume":"13","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3344-9328","authenticated-orcid":false,"given":"Brianna","family":"Atto","sequence":"first","affiliation":[{"name":"School of Health Sciences, University of Tasmania, Launceston, TAS 7248, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yitayal","family":"Anteneh","sequence":"additional","affiliation":[{"name":"Child and Maternal Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT 0811, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9474-6943","authenticated-orcid":false,"given":"Seweryn","family":"Bialasiewicz","sequence":"additional","affiliation":[{"name":"Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5455-690X","authenticated-orcid":false,"given":"Michael J.","family":"Binks","sequence":"additional","affiliation":[{"name":"Child and Maternal Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT 0811, Australia"},{"name":"SAHMRI Women and Kids, South Australian Health and Medical Research Institute, Adelaide, SA 5000, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0003-0433-7778","authenticated-orcid":false,"given":"Mostafa","family":"Hashemi","sequence":"additional","affiliation":[{"name":"Department of Chemical and Biological Engineering, The University of British Columbia, Vancouver, BC V6T 1Z3, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jane","family":"Hill","sequence":"additional","affiliation":[{"name":"Department of Chemical and Biological Engineering, The University of British Columbia, Vancouver, BC V6T 1Z3, Canada"},{"name":"Spire Health Technology, PBC, Seattle, WA 98195, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ruth B.","family":"Thornton","sequence":"additional","affiliation":[{"name":"Centre for Child Health Research, University of Western Australia, Perth, WA 6009, Australia"},{"name":"Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, Perth, WA 6009, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jacob","family":"Westaway","sequence":"additional","affiliation":[{"name":"Child and Maternal Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT 0811, Australia"},{"name":"Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Cairns, QLD 4811, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8507-6586","authenticated-orcid":false,"given":"Robyn L.","family":"Marsh","sequence":"additional","affiliation":[{"name":"School of Health Sciences, University of Tasmania, Launceston, TAS 7248, Australia"},{"name":"Child and Maternal Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT 0811, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2023,12,28]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","unstructured":"Bergmann, M., Haasenritter, J., Beidatsch, D., Schwarm, S., H\u00f6rner, K., B\u00f6sner, S., Grevenrath, P., Schmidt, L., Viniol, A., and Donner-Banzhoff, N. (2021). Coughing children in family practice and primary care: A systematic review of prevalence, aetiology and prognosis. BMC Pediatr., 21.","DOI":"10.1186\/s12887-021-02739-4"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"21","DOI":"10.5694\/mja14.00287","article-title":"Chronic suppurative lung disease and bronchiectasis in children and adults in Australia and New Zealand Thoracic Society of Australia and New Zealand guidelines","volume":"202","author":"Chang","year":"2015","journal-title":"Med. J. Aust."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"1602139","DOI":"10.1183\/13993003.02139-2016","article-title":"ERS statement on protracted bacterial bronchitis in children","volume":"50","author":"Kantar","year":"2017","journal-title":"Eur. Respir. J."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"1044","DOI":"10.1136\/archdischild-2017-312848","article-title":"Chronic cough postacute respiratory illness in children: A cohort study","volume":"102","author":"Drescher","year":"2017","journal-title":"Arch. Dis. Child."},{"key":"ref_5","doi-asserted-by":"crossref","unstructured":"O\u2019Grady, K.-A.F., Mahon, J., Arnold, D., Grimwood, K., Hall, K.K., Goyal, V., Marchant, J.M., Phillips, N., Acworth, J., and King, A. (2021). Predictors of the development of protracted bacterial bronchitis following presentation to healthcare for an acute respiratory illness with cough: Analysis of three cohort studies. J. Clin. Med., 10.","DOI":"10.3390\/jcm10245735"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"1101","DOI":"10.1016\/j.chest.2016.06.030","article-title":"Protracted Bacterial Bronchitis in Children: Natural History and Risk Factors for Bronchiectasis","volume":"150","author":"Wurzel","year":"2016","journal-title":"Chest"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"241","DOI":"10.1111\/resp.13950","article-title":"Outcomes of protracted bacterial bronchitis in children: A 5-year prospective cohort study","volume":"26","author":"Ruffles","year":"2021","journal-title":"Respirology"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"2707","DOI":"10.1002\/ppul.25438","article-title":"Chronic wet cough in Australian children: Societal costs and quality of life","volume":"56","author":"Prime","year":"2021","journal-title":"Pediatr. Pulmonol."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"1396","DOI":"10.1016\/j.chest.2023.06.040","article-title":"The Economic Burden of Bronchiectasis: A Systematic Review","volume":"164","author":"Roberts","year":"2023","journal-title":"Chest"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"130","DOI":"10.1080\/15412550902766934","article-title":"Phenotypes of adult bronchiectasis: Onset of productive cough in childhood and adulthood","volume":"6","author":"King","year":"2009","journal-title":"COPD J. Chronic Obstr. Pulm. Dis."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"7","DOI":"10.4103\/atm.ATM_12_17","article-title":"An underestimated cause of chronic cough: The protracted bacterial bronchitis","volume":"13","author":"Scaparrotta","year":"2018","journal-title":"Ann. Thorac. Med."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"339","DOI":"10.1111\/resp.14479","article-title":"Thoracic Society of Australia and New Zealand (TSANZ) position statement on chronic suppurative lung disease and bronchiectasis in children, adolescents and adults in Australia and New Zealand","volume":"28","author":"Chang","year":"2023","journal-title":"Respirology"},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"433","DOI":"10.3389\/fped.2020.00433","article-title":"When the cough does not improve: A review on protracted bacterial bronchitis in children","volume":"8","author":"Gallucci","year":"2020","journal-title":"Front. Pediatr."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"621","DOI":"10.1016\/j.jpeds.2012.03.049","article-title":"Pulmonary innate immunity in children with protracted bacterial bronchitis","volume":"161","author":"Chang","year":"2012","journal-title":"J. Pediatr."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"1092","DOI":"10.1002\/ppul.20906","article-title":"Prospective assessment of protracted bacterial bronchitis: Airway inflammation and innate immune activation","volume":"43","author":"Marchant","year":"2008","journal-title":"Pediatr. Pulmonol."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"1673","DOI":"10.1378\/chest.129.6.1673","article-title":"Burying the dead: The impact of failed apoptotic cell removal (efferocytosis) on chronic inflammatory lung disease","volume":"129","author":"Vandivier","year":"2006","journal-title":"Chest"},{"key":"ref_17","doi-asserted-by":"crossref","unstructured":"Kartsiouni, E., Chatzipanagiotou, S., Galani, A., Moriki, D., Sardeli, O., Prountzos, S., Alexopoulou, E., Loukou, I., Priftis, K.N., and Douros, K. (2022). Clinical course of children with chronic suppurative lung disease or bronchiectasis infected with Pseudomonas aeruginosa. Children, 9.","DOI":"10.22541\/au.164174484.46396659\/v1"},{"key":"ref_18","first-page":"6","article-title":"Inflammation: A two-edged sword\u2014The model of bronchiectasis","volume":"147","author":"Cole","year":"1986","journal-title":"Eur. J. Respir. Diseases. Suppl."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"123","DOI":"10.3389\/fped.2017.00123","article-title":"Bronchiectasis in children: Current concepts in immunology and microbiology","volume":"5","author":"Pizzutto","year":"2017","journal-title":"Front. Pediatr."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"499","DOI":"10.1055\/s-0041-1730891","article-title":"Pathophysiology of Bronchiectasis","volume":"42","author":"Keir","year":"2021","journal-title":"Semin. Respir. Crit. Care Med."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"880","DOI":"10.1016\/S0140-6736(18)31767-7","article-title":"Advances in bronchiectasis: Endotyping, genetics, microbiome, and disease heterogeneity","volume":"392","author":"Flume","year":"2018","journal-title":"Lancet"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"505","DOI":"10.1016\/j.pulmoe.2023.03.004","article-title":"Endotypes in bronchiectasis: Moving towards precision medicine. A narrative review","volume":"29","author":"Martins","year":"2023","journal-title":"Pulmonology"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"1311","DOI":"10.1016\/j.chom.2022.08.005","article-title":"Neisseria species as pathobionts in bronchiectasis","volume":"30","author":"Li","year":"2022","journal-title":"Cell Host Microbe"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"88","DOI":"10.1016\/j.jpeds.2011.06.049","article-title":"Protracted bacterial bronchitis in young children: Association with airway malacia","volume":"160","author":"Kompare","year":"2012","journal-title":"J. Pediatr."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"224","DOI":"10.1002\/ppul.23931","article-title":"Defining lower airway bacterial infection in children with chronic endobronchial disorders","volume":"53","author":"Hare","year":"2018","journal-title":"Pediatr. Pulmonol."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"72","DOI":"10.1136\/archdischild-2012-302760","article-title":"Protracted bacterial bronchitis: Reinventing an old disease","volume":"98","author":"Craven","year":"2013","journal-title":"Arch. Dis. Child."},{"key":"ref_27","doi-asserted-by":"crossref","unstructured":"Broderick, D.T.J., Waite, D.W., Marsh, R.L., Camargo, C.A., Cardenas, P., Chang, A.B., Cookson, W.O.C., Cuthbertson, L., Dai, W., and Everard, M.L. (2021). Bacterial Signatures of Paediatric Respiratory Disease: An Individual Participant Data Meta-Analysis. Front. Microbiol., 12.","DOI":"10.3389\/fmicb.2021.711134"},{"key":"ref_28","doi-asserted-by":"crossref","unstructured":"Cuthbertson, L., Craven, V., Bingle, L., Cookson, W.O., Everard, M.L., and Moffatt, M.F. (2017). The impact of persistent bacterial bronchitis on the pulmonary microbiome of children. PLoS ONE, 12.","DOI":"10.1101\/181982"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"778","DOI":"10.1016\/j.chest.2019.01.002","article-title":"Multiple respiratory microbiota profiles are associated with lower airway inflammation in children with protracted bacterial bronchitis","volume":"155","author":"Marsh","year":"2019","journal-title":"Chest"},{"key":"ref_30","doi-asserted-by":"crossref","unstructured":"Marsh, R.L., Kaestli, M., Chang, A.B., Binks, M.J., Pope, C.E., Hoffman, L.R., and Smith-Vaughan, H.C. (2016). The microbiota in bronchoalveolar lavage from young children with chronic lung disease includes taxa present in both the oropharynx and nasopharynx. Microbiome, 4.","DOI":"10.1186\/s40168-016-0182-1"},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"1900704","DOI":"10.1183\/13993003.00704-2019","article-title":"The airway microbiota in children newly diagnosed with bronchiectasis largely retains its diversity","volume":"54","author":"Pillarisetti","year":"2019","journal-title":"Eur. Respir. J."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"1039","DOI":"10.1513\/AnnalsATS.201312-456OC","article-title":"Three clinically distinct chronic pediatric airway infections share a common core microbiota","volume":"11","author":"Cuthbertson","year":"2014","journal-title":"Ann. Am. Thorac. Soc."},{"key":"ref_33","doi-asserted-by":"crossref","unstructured":"Broderick, D.T.J., Regtien, T., Ainsworth, A., Taylor, M.W., and Pillarisetti, N. (2021). Dynamic Upper and Lower Airway Microbiotas in Paediatric Bronchiectasis Exacerbations: A Pilot Study. Front. Cell. Infect. Microbiol., 11.","DOI":"10.3389\/fcimb.2021.773496"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"1147","DOI":"10.1164\/rccm.202303-0499OC","article-title":"Inflammatory Molecular Endotypes in Bronchiectasis: A European Multicenter Cohort Study","volume":"208","author":"Choi","year":"2023","journal-title":"Am. J. Respir. Crit. Care Med."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"957","DOI":"10.1164\/rccm.201104-0655OC","article-title":"Topographical continuity of bacterial populations in the healthy human respiratory tract","volume":"184","author":"Charlson","year":"2011","journal-title":"Am. J. Respir. Crit. Care Med."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"e215","DOI":"10.1016\/S2666-5247(21)00300-1","article-title":"Prevalence and subtyping of biofilms present in bronchoalveolar lavage from children with protracted bacterial bronchitis or non-cystic fibrosis bronchiectasis: A cross-sectional study","volume":"3","author":"Marsh","year":"2022","journal-title":"Lancet Microbe"},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"190048","DOI":"10.1183\/16000617.0048-2019","article-title":"The microbiome in bronchiectasis","volume":"28","author":"Richardson","year":"2019","journal-title":"Eur. Respir. Rev."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"2227","DOI":"10.1016\/j.celrep.2019.01.091","article-title":"Human and Extracellular DNA Depletion for Metagenomic Analysis of Complex Clinical Infection Samples Yields Optimized Viable Microbiome Profiles","volume":"26","author":"Nelson","year":"2019","journal-title":"Cell Rep."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"396","DOI":"10.1097\/INF.0000000000003865","article-title":"A Hypothesis-Generating Prospective Longitudinal Study to Assess the Relative Contribution of Common Respiratory Viruses to Severe Lower Respiratory Infections in Young Children","volume":"42","author":"Ramilo","year":"2023","journal-title":"Pediatr. Infect. Dis. J."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"749","DOI":"10.1136\/archdischild-2013-305147","article-title":"Respiratory viruses in exacerbations of non-cystic fibrosis bronchiectasis in children","volume":"99","author":"Kapur","year":"2014","journal-title":"Arch. Dis. Child."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"1200","DOI":"10.1016\/j.chest.2021.04.057","article-title":"Comparison of profiles of first nations and non-first nations children with bronchiectasis over two 5-year periods in the Northern Territory, Australia","volume":"160","author":"McCallum","year":"2021","journal-title":"Chest"},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"330","DOI":"10.1016\/j.jcv.2008.08.003","article-title":"WU and KI polyomavirus present in the respiratory tract of children, but not in immunocompetent adults","volume":"43","author":"Ren","year":"2008","journal-title":"J. Clin. Virol."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"969","DOI":"10.1136\/thoraxjnl-2017-210233","article-title":"Viruses causing lower respiratory symptoms in young children: Findings from the ORChID birth cohort","volume":"73","author":"Sarna","year":"2018","journal-title":"Thorax"},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"704","DOI":"10.1016\/j.chom.2015.03.008","article-title":"The infant nasopharyngeal microbiome impacts severity of lower respiratory infection and risk of asthma development","volume":"17","author":"Teo","year":"2015","journal-title":"Cell Host Microbe"},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"265","DOI":"10.3389\/fped.2019.00265","article-title":"Lung microbiota and pulmonary inflammatory cytokines expression vary in children with tracheomalacia and adenoviral or mycoplasma pneumoniae pneumonia","volume":"7","author":"Wang","year":"2019","journal-title":"Front. Pediatr."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"55","DOI":"10.1016\/j.rmed.2019.04.003","article-title":"Detecting respiratory viruses in children with protracted bacterial bronchitis","volume":"151","author":"Wang","year":"2019","journal-title":"Respir. Med."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"34","DOI":"10.1093\/cid\/ciu225","article-title":"Adenovirus species C is associated with chronic suppurative lung diseases in children","volume":"59","author":"Wurzel","year":"2014","journal-title":"Clin. Infect. Dis."},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"613","DOI":"10.1002\/ppul.23342","article-title":"Risk factors for adverse outcomes of Indigenous infants hospitalized with bronchiolitis","volume":"51","author":"McCallum","year":"2016","journal-title":"Pediatr. Pulmonol."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"10608","DOI":"10.1128\/JVI.76.21.10608-10616.2002","article-title":"Prevalence and quantitation of species C adenovirus DNA in human mucosal lymphocytes","volume":"76","author":"Garnett","year":"2002","journal-title":"J. Virol."},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"1271","DOI":"10.1378\/chest.13-2442","article-title":"Prospective characterization of protracted bacterial bronchitis in children","volume":"145","author":"Wurzel","year":"2014","journal-title":"Chest"},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"72","DOI":"10.1136\/jcp.24.1.72","article-title":"Bronchiolitis obliterans, bronchiectasis, and other sequelae of adenovirus type 21 infection in young children","volume":"24","author":"Becroft","year":"1971","journal-title":"J. Clin. Pathol."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"719","DOI":"10.1016\/j.chom.2019.04.001","article-title":"Redondoviridae, a family of small, circular DNA viruses of the human oro-respiratory tract associated with periodontitis and critical illness","volume":"25","author":"Abbas","year":"2019","journal-title":"Cell Host Microbe"},{"key":"ref_53","doi-asserted-by":"crossref","unstructured":"Dodi, G., Attanasi, M., Di Filippo, P., Di Pillo, S., and Chiarelli, F. (2021). Virome in the lungs: The role of anelloviruses in childhood respiratory diseases. Microorganisms, 9.","DOI":"10.3390\/microorganisms9071357"},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"971","DOI":"10.1086\/423143","article-title":"Correlation between Torque tenovirus infection and serum levels of eosinophil cationic protein in children hospitalized for acute respiratory diseases","volume":"190","author":"Maggi","year":"2004","journal-title":"J. Infect. Dis."},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"1084002","DOI":"10.3389\/fmed.2023.1084002","article-title":"Predictors of pulmonary sequelae after COVID-19 pneumonia: A 12-month follow-up study","volume":"10","author":"Bernardinello","year":"2023","journal-title":"Front. Med."},{"key":"ref_56","doi-asserted-by":"crossref","unstructured":"Ribeiro Carvalho, C.R., Lamas, C.A., Chate, R.C., Salge, J.M., Sawamura, M.V.Y., de Albuquerque, A.L., Toufen Junior, C., Lima, D.M., Garcia, M.L., and Scudeller, P.G. (2023). Long-term respiratory follow-up of ICU hospitalized COVID-19 patients: Prospective cohort study. PLoS ONE, 18.","DOI":"10.1371\/journal.pone.0280567"},{"key":"ref_57","doi-asserted-by":"crossref","unstructured":"Dadali, Y., \u00d6zka\u00e7maz, S., \u00dcnl\u00fc, E., Akyol, R., and Alparslan, M. (2022). Computed tomography findings of COVID-19 in pediatric patients. Turk. J. Pediatr., 64.","DOI":"10.24953\/turkjped.2021.1726"},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1093\/cid\/cir766","article-title":"Bronchiectasis is associated with human T-lymphotropic virus 1 infection in an Indigenous Australian population","volume":"54","author":"Einsiedel","year":"2012","journal-title":"Clin. Infect. Dis."},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"617240","DOI":"10.3389\/falgy.2020.617240","article-title":"Interactions of bacteriophages and bacteria at the airway mucosa: New insights into the pathophysiology of asthma","volume":"1","author":"Skliros","year":"2021","journal-title":"Front. Allergy"},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"300","DOI":"10.1002\/ppul.21550","article-title":"Lower airway microbiology and cellularity in children with newly diagnosed non-CF bronchiectasis","volume":"47","author":"Kapur","year":"2012","journal-title":"Pediatr. Pulmonol."},{"key":"ref_61","doi-asserted-by":"crossref","unstructured":"Thornton, R.B., Wiertsema, S.P., Kirkham, L.-A.S., Rigby, P.J., Vijayasekaran, S., Coates, H.L., and Richmond, P.C. (2013). Neutrophil extracellular traps and bacterial biofilms in middle ear effusion of children with recurrent acute otitis media\u2014A potential treatment target. PLoS ONE, 8.","DOI":"10.1371\/journal.pone.0053837"},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"2148","DOI":"10.1111\/jam.15049","article-title":"Diagnosis of biofilm infections: Current methods used, challenges and perspectives for the future","volume":"131","author":"Silva","year":"2021","journal-title":"J. Appl. Microbiol."},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1016\/j.molimm.2012.09.011","article-title":"Mechanisms of immune dysfunction and bacterial persistence in non-cystic fibrosis bronchiectasis","volume":"55","author":"Chalmers","year":"2013","journal-title":"Mol. Immunol."},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"862","DOI":"10.1093\/infdis\/155.5.862","article-title":"Diagnosing bacterial respiratory infection by bronchoalveolar lavage","volume":"155","author":"Kahn","year":"1987","journal-title":"J. Infect. Dis."},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"1174","DOI":"10.1183\/09031936.96.09061174","article-title":"Measurement of inflammatory indices in induced sputum: Effects of selection of sputum to minimize salivary contamination","volume":"9","author":"Pizzichini","year":"1996","journal-title":"Eur. Respir. J."},{"key":"ref_66","doi-asserted-by":"crossref","first-page":"284","DOI":"10.1002\/ppul.23031","article-title":"Detection of biofilm in bronchoalveolar lavage from children with non-cystic fibrosis bronchiectasis","volume":"50","author":"Marsh","year":"2015","journal-title":"Pediatr. Pulmonol."},{"key":"ref_67","doi-asserted-by":"crossref","unstructured":"Welp, A.L., and Bomberger, J.M. (2020). Bacterial community interactions during chronic respiratory disease. Front. Cell. Infect. Microbiol., 10.","DOI":"10.3389\/fcimb.2020.00213"},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"1001","DOI":"10.1016\/j.jpeds.2010.06.002","article-title":"Respiratory bacterial pathogens in the nasopharynx and lower airways of Australian indigenous children with bronchiectasis","volume":"157","author":"Hare","year":"2010","journal-title":"J. Pediatr."},{"key":"ref_69","doi-asserted-by":"crossref","first-page":"549","DOI":"10.1093\/infdis\/jiq087","article-title":"Divergent mechanisms for passive pneumococcal resistance to \u03b2-lactam antibiotics in the presence of Haemophilus influenzae","volume":"203","author":"Weimer","year":"2011","journal-title":"J. Infect. Dis."},{"key":"ref_70","doi-asserted-by":"crossref","first-page":"3845","DOI":"10.1128\/AAC.01772-10","article-title":"Moraxella catarrhalis outer membrane vesicles carry \u03b2-lactamase and promote survival of Streptococcus pneumoniae and Haemophilus influenzae by inactivating amoxicillin","volume":"55","author":"Schaar","year":"2011","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_71","doi-asserted-by":"crossref","first-page":"280","DOI":"10.1111\/2049-632X.12129","article-title":"Residence of Streptococcus pneumoniae and Moraxella catarrhalis within polymicrobial biofilm promotes antibiotic resistance and bacterial persistence in vivo","volume":"70","author":"Perez","year":"2014","journal-title":"Pathog. Dis."},{"key":"ref_72","doi-asserted-by":"crossref","unstructured":"Tikhomirova, A., Zilm, P.S., Trappetti, C., Paton, J.C., and Kidd, S.P. (2022). The central role of arginine in Haemophilus influenzae survival in a polymicrobial environment with Streptococcus pneumoniae and Moraxella catarrhalis. PLoS ONE, 17.","DOI":"10.1371\/journal.pone.0271912"},{"key":"ref_73","doi-asserted-by":"crossref","first-page":"218","DOI":"10.1186\/s13568-017-0521-z","article-title":"Inhibitory effect of streptococci on the growth of M. catarrhalis strains and the diversity of putative bacteriocin-like gene loci in the genomes of S. pneumoniae and its relatives","volume":"7","author":"Ikryannikova","year":"2017","journal-title":"AMB Express"},{"key":"ref_74","doi-asserted-by":"crossref","first-page":"114","DOI":"10.1111\/2049-632X.12073","article-title":"Haemophilus influenzae and Streptococcus pneumoniae: Living together in a biofilm","volume":"69","author":"Tikhomirova","year":"2013","journal-title":"Pathog. Dis."},{"key":"ref_75","doi-asserted-by":"crossref","unstructured":"Bair, K.L., and Campagnari, A.A. (2020). Moraxella catarrhalis promotes stable polymicrobial biofilms with the major otopathogens. Front. Microbiol., 10.","DOI":"10.3389\/fmicb.2019.03006"},{"key":"ref_76","doi-asserted-by":"crossref","first-page":"1663","DOI":"10.1042\/CS20181009","article-title":"New therapeutic targets for the prevention of infectious acute exacerbations of COPD: Role of epithelial adhesion molecules and inflammatory pathways","volume":"133","author":"Atto","year":"2019","journal-title":"Clin. Sci."},{"key":"ref_77","doi-asserted-by":"crossref","first-page":"191","DOI":"10.1046\/j.1462-5822.2002.00180.x","article-title":"Molecular and cellular determinants of non-typeable Haemophilus influenzae adherence and invasion","volume":"4","year":"2002","journal-title":"Cell. Microbiol."},{"key":"ref_78","doi-asserted-by":"crossref","first-page":"392","DOI":"10.1128\/IAI.01168-12","article-title":"Microbial modulation of host immunity with the small molecule phosphorylcholine","volume":"81","author":"Clark","year":"2013","journal-title":"Infect. Immun."},{"key":"ref_79","unstructured":"Cundell, D.R., Gerard, C., Idanpaan-Heikkila, I., Tuomanen, E.I., and Gerard, N.P. (1996). Platelet-Activating Factor and Related Lipid Mediators 2: Roles in Health and Disease, Plenum Press."},{"key":"ref_80","doi-asserted-by":"crossref","first-page":"1270","DOI":"10.1038\/ni.1661","article-title":"CEACAM1 inhibits Toll-like receptor 2\u2013triggered antibacterial responses of human pulmonary epithelial cells","volume":"9","author":"Slevogt","year":"2008","journal-title":"Nat. Immunol."},{"key":"ref_81","doi-asserted-by":"crossref","first-page":"830","DOI":"10.1128\/IAI.74.2.830-838.2006","article-title":"Nontypeable Haemophilus influenzae adheres to intercellular adhesion molecule 1 (ICAM-1) on respiratory epithelial cells and upregulates ICAM-1 expression","volume":"74","author":"Avadhanula","year":"2006","journal-title":"Infect. Immun."},{"key":"ref_82","doi-asserted-by":"crossref","unstructured":"Pickering, J.L., Prosser, A., Corscadden, K.J., de Gier, C., Richmond, P.C., Zhang, G., Thornton, R.B., and Kirkham, L.A. (2016). Haemophilus haemolyticus Interaction with Host Cells Is Different to Nontypeable Haemophilus influenzae and Prevents NTHi Association with Epithelial Cells. Front. Cell. Infect. Microbiol., 6.","DOI":"10.3389\/fcimb.2016.00050"},{"key":"ref_83","doi-asserted-by":"crossref","unstructured":"Atto, B., Kunde, D., Gell, D.A., and Tristram, S. (2021). Haemophilin-Producing Strains of Haemophilus haemolyticus Protect Respiratory Epithelia from NTHi Colonisation and Internalisation. Pathogens, 10.","DOI":"10.3390\/pathogens10010029"},{"key":"ref_84","doi-asserted-by":"crossref","first-page":"e01725-15","DOI":"10.1128\/mBio.01725-15","article-title":"Corynebacterium accolens Releases Antipneumococcal Free Fatty Acids from Human Nostril and Skin Surface Triacylglycerols","volume":"7","author":"Bomar","year":"2016","journal-title":"mBio"},{"key":"ref_85","doi-asserted-by":"crossref","first-page":"140","DOI":"10.1016\/j.ijantimicag.2015.12.004","article-title":"Production of extended-spectrum beta-lactamases and the potential indirect pathogenic role of Prevotella isolates from the cystic fibrosis respiratory microbiota","volume":"47","author":"Sherrard","year":"2016","journal-title":"Int. J. Antimicrob. Agents"},{"key":"ref_86","doi-asserted-by":"crossref","first-page":"515","DOI":"10.1034\/j.1600-0463.2002.11007801.x","article-title":"Mixed microbial aetiology of community-acquired pneumonia in children","volume":"110","author":"Korppi","year":"2002","journal-title":"Apmis"},{"key":"ref_87","doi-asserted-by":"crossref","unstructured":"Gu, L., Deng, H., Ren, Z., Zhao, Y., Yu, S., Guo, Y., Dai, J., Chen, X., Li, K., and Li, R. (2019). Dynamic changes in the microbiome and mucosal immune microenvironment of the lower respiratory tract by influenza virus infection. Front. Microbiol., 10.","DOI":"10.3389\/fmicb.2019.02491"},{"key":"ref_88","doi-asserted-by":"crossref","first-page":"1224","DOI":"10.1164\/rccm.201302-0341OC","article-title":"Outgrowth of the bacterial airway microbiome after rhinovirus exacerbation of chronic obstructive pulmonary disease","volume":"188","author":"Molyneaux","year":"2013","journal-title":"Am. J. Respir. Crit. Care Med."},{"key":"ref_89","doi-asserted-by":"crossref","first-page":"984","DOI":"10.1136\/jim-2017-000414","article-title":"Nasopharyngeal microbiome in premature infants and stability during rhinovirus infection","volume":"65","author":"Perez","year":"2017","journal-title":"J. Investig. Med."},{"key":"ref_90","doi-asserted-by":"crossref","first-page":"1045","DOI":"10.1093\/cid\/cix941","article-title":"Dynamics of bacterial colonization with Streptococcus pneumoniae, Haemophilus influenzae, and Moraxella catarrhalis during symptomatic and asymptomatic viral upper respiratory tract infection","volume":"66","author":"DeMuri","year":"2018","journal-title":"Clin. Infect. Dis."},{"key":"ref_91","doi-asserted-by":"crossref","unstructured":"Binks, M.J., Cheng, A.C., Smith-Vaughan, H., Sloots, T., Nissen, M., Whiley, D., McDonnell, J., and Leach, A.J. (2011). Viral-bacterial co-infection in Australian Indigenous children with acute otitis media. BMC Infect. Dis., 11.","DOI":"10.1186\/1471-2334-11-161"},{"key":"ref_92","doi-asserted-by":"crossref","first-page":"1328","DOI":"10.1038\/s41564-019-0447-0","article-title":"Direct interactions with influenza promote bacterial adherence during respiratory infections","volume":"4","author":"Rowe","year":"2019","journal-title":"Nat. Microbiol."},{"key":"ref_93","doi-asserted-by":"crossref","first-page":"1040","DOI":"10.1164\/arrd.1986.134.5.1040","article-title":"Adherence of type I Streptococcus pneumoniae to tracheal epithelium of mice infected with influenza A\/PR8 virus","volume":"134","author":"Plotkowski","year":"1986","journal-title":"Am. Rev. Respir. Dis."},{"key":"ref_94","doi-asserted-by":"crossref","first-page":"84","DOI":"10.1111\/j.1574-6968.2010.02049.x","article-title":"Fosfomycin suppresses RS-virus-induced Streptococcus pneumoniae and Haemophilus influenzae adhesion to respiratory epithelial cells via the platelet-activating factor receptor","volume":"310","author":"Yokota","year":"2010","journal-title":"FEMS Microbiol. Lett."},{"key":"ref_95","doi-asserted-by":"crossref","first-page":"e00248-20","DOI":"10.1128\/IAI.00248-20","article-title":"Nontypeable haemophilus influenzae type IV pilus mediates augmented adherence to rhinovirus-infected human airway epithelial cells","volume":"88","author":"Toone","year":"2020","journal-title":"Infect. Immun."},{"key":"ref_96","doi-asserted-by":"crossref","first-page":"109267","DOI":"10.1016\/j.celrep.2021.109267","article-title":"Streptococcus pneumoniae binds to host GAPDH on dying lung epithelial cells worsening secondary infection following influenza","volume":"35","author":"Park","year":"2021","journal-title":"Cell Rep."},{"key":"ref_97","doi-asserted-by":"crossref","first-page":"e00384-20","DOI":"10.1128\/mSphere.00384-20","article-title":"Nontypeable Haemophilus influenzae responds to virus-infected cells with a significant increase in type IV pilus expression","volume":"5","author":"Mokrzan","year":"2020","journal-title":"mSphere"},{"key":"ref_98","doi-asserted-by":"crossref","first-page":"1250","DOI":"10.4049\/jimmunol.1300014","article-title":"Depletion of alveolar macrophages during influenza infection facilitates bacterial superinfections","volume":"191","author":"Ghoneim","year":"2013","journal-title":"J. Immunol."},{"key":"ref_99","doi-asserted-by":"crossref","first-page":"843","DOI":"10.1038\/s41385-019-0160-6","article-title":"Microbes, metabolites, and the gut\u2013lung axis","volume":"12","author":"Dang","year":"2019","journal-title":"Mucosal Immunol."},{"key":"ref_100","doi-asserted-by":"crossref","first-page":"e00251-12","DOI":"10.1128\/mBio.00251-12","article-title":"Serial analysis of the gut and respiratory microbiome in cystic fibrosis in infancy: Interaction between intestinal and respiratory tracts and impact of nutritional exposures","volume":"3","author":"Madan","year":"2012","journal-title":"mBio"},{"key":"ref_101","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1038\/mi.2011.55","article-title":"Pulmonary-intestinal cross-talk in mucosal inflammatory disease","volume":"5","author":"Keely","year":"2012","journal-title":"Mucosal Immunol."},{"key":"ref_102","doi-asserted-by":"crossref","first-page":"6794","DOI":"10.3748\/wjg.v19.i40.6794","article-title":"Gut-lung crosstalk in pulmonary involvement with inflammatory bowel diseases","volume":"19","author":"Wang","year":"2013","journal-title":"World J. Gastroenterol. WJG"},{"key":"ref_103","doi-asserted-by":"crossref","first-page":"1511","DOI":"10.1111\/j.1572-0241.2001.03748.x","article-title":"Respiratory symptoms and pulmonary functional changes in patients with irritable bowel syndrome","volume":"96","author":"Yazar","year":"2001","journal-title":"Am. J. Gastroenterol."},{"key":"ref_104","doi-asserted-by":"crossref","first-page":"159","DOI":"10.1038\/nm.3444","article-title":"Gut microbiota metabolism of dietary fiber influences allergic airway disease and hematopoiesis","volume":"20","author":"Trompette","year":"2014","journal-title":"Nat. Med."},{"key":"ref_105","doi-asserted-by":"crossref","first-page":"e133","DOI":"10.1038\/cti.2017.6","article-title":"Microbiome effects on immunity, health and disease in the lung","volume":"6","author":"Shukla","year":"2017","journal-title":"Clin. Transl. Immunol."},{"key":"ref_106","doi-asserted-by":"crossref","first-page":"1871","DOI":"10.1084\/jem.20122762","article-title":"Lung dendritic cells induce migration of protective T cells to the gastrointestinal tract","volume":"210","author":"Ruane","year":"2013","journal-title":"J. Exp. Med."},{"key":"ref_107","doi-asserted-by":"crossref","first-page":"1678","DOI":"10.3389\/fimmu.2017.01678","article-title":"Protective microbiota: From localized to long-reaching co-immunity","volume":"8","author":"Chiu","year":"2017","journal-title":"Front. Immunol."},{"key":"ref_108","doi-asserted-by":"crossref","unstructured":"Grier, A., McDavid, A., Wang, B., Qiu, X., Java, J., Bandyopadhyay, S., Yang, H., Holden-Wiltse, J., Kessler, H.A., and Gill, A.L. (2018). Neonatal gut and respiratory microbiota: Coordinated development through time and space. Microbiome, 6.","DOI":"10.1186\/s40168-018-0566-5"},{"key":"ref_109","doi-asserted-by":"crossref","first-page":"263","DOI":"10.1038\/nrgastro.2017.34","article-title":"Gut microbiota: Neonatal gut microbiota induces lung immunity against pneumonia","volume":"14","author":"Tamburini","year":"2017","journal-title":"Nat. Rev. Gastroenterol. Hepatol."},{"key":"ref_110","doi-asserted-by":"crossref","first-page":"eaaf9412","DOI":"10.1126\/scitranslmed.aaf9412","article-title":"Intestinal commensal bacteria mediate lung mucosal immunity and promote resistance of newborn mice to infection","volume":"9","author":"Gray","year":"2017","journal-title":"Sci. Transl. Med."},{"key":"ref_111","doi-asserted-by":"crossref","first-page":"1630","DOI":"10.1038\/s41401-020-00573-5","article-title":"Probiotics protect against RSV infection by modulating the microbiota-alveolar-macrophage axis","volume":"42","author":"Ji","year":"2021","journal-title":"Acta Pharmacol. Sin."},{"key":"ref_112","doi-asserted-by":"crossref","first-page":"1098","DOI":"10.1016\/j.immuni.2023.03.002","article-title":"Maternal diet modulates the infant microbiome and intestinal Flt3L necessary for dendritic cell development and immunity to respiratory infection","volume":"56","author":"Sikder","year":"2023","journal-title":"Immunity"},{"key":"ref_113","doi-asserted-by":"crossref","unstructured":"Zhang, D., Li, S., Wang, N., Tan, H.-Y., Zhang, Z., and Feng, Y. (2020). The cross-talk between gut microbiota and lungs in common lung diseases. Front. Microbiol., 11.","DOI":"10.3389\/fmicb.2020.00301"},{"key":"ref_114","doi-asserted-by":"crossref","first-page":"3589","DOI":"10.1038\/s41598-020-60015-4","article-title":"Respiratory mycobiome and suggestion of inter-kingdom network during acute pulmonary exacerbation in cystic fibrosis","volume":"10","author":"Soret","year":"2020","journal-title":"Sci. Rep."},{"key":"ref_115","doi-asserted-by":"crossref","unstructured":"Frati, F., Salvatori, C., Incorvaia, C., Bellucci, A., Di Cara, G., Marcucci, F., and Esposito, S. (2018). The role of the microbiome in asthma: The gut\u2013lung axis. Int. J. Mol. Sci., 20.","DOI":"10.3390\/ijms20010123"},{"key":"ref_116","doi-asserted-by":"crossref","first-page":"4217","DOI":"10.1128\/JCM.01967-14","article-title":"Severity-related changes of bronchial microbiome in chronic obstructive pulmonary disease","volume":"52","author":"Millares","year":"2014","journal-title":"J. Clin. Microbiol."},{"key":"ref_117","doi-asserted-by":"crossref","first-page":"908","DOI":"10.1164\/rccm.202205-0893OC","article-title":"Microbial Dysregulation of the Gut-Lung Axis in Bronchiectasis","volume":"207","author":"Narayana","year":"2023","journal-title":"Am. J. Respir. Crit. Care Med."},{"key":"ref_118","doi-asserted-by":"crossref","first-page":"516","DOI":"10.1067\/mai.2001.118130","article-title":"Allergy development and the intestinal microflora during the first year of life","volume":"108","author":"Sepp","year":"2001","journal-title":"J. Allergy Clin. Immunol."},{"key":"ref_119","doi-asserted-by":"crossref","first-page":"2199","DOI":"10.1042\/CS20160349","article-title":"Shifts in Lachnospira and Clostridium sp. in the 3-month stool microbiome are associated with preschool age asthma","volume":"130","author":"Stiemsma","year":"2016","journal-title":"Clin. Sci."},{"key":"ref_120","doi-asserted-by":"crossref","first-page":"1187","DOI":"10.1038\/nm.4176","article-title":"Neonatal gut microbiota associates with childhood multisensitized atopy and T cell differentiation","volume":"22","author":"Fujimura","year":"2016","journal-title":"Nat. Med."},{"key":"ref_121","doi-asserted-by":"crossref","first-page":"129","DOI":"10.1067\/mai.2001.111237","article-title":"Distinct patterns of neonatal gut microflora in infants in whom atopy was and was not developing","volume":"107","author":"Kirjavainen","year":"2001","journal-title":"J. Allergy Clin. Immunol."},{"key":"ref_122","doi-asserted-by":"crossref","first-page":"365","DOI":"10.1164\/rccm.202205-0860ED","article-title":"Microbiomics-focused Data Integration: A Fresh Solve for the Rubik\u2019s Cube of Endophenotyping?","volume":"206","author":"Narayana","year":"2022","journal-title":"Am. J. Respir. Crit. Care Med."},{"key":"ref_123","doi-asserted-by":"crossref","first-page":"783","DOI":"10.1038\/s41587-019-0156-5","article-title":"Nanopore metagenomics enables rapid clinical diagnosis of bacterial lower respiratory infection","volume":"37","author":"Charalampous","year":"2019","journal-title":"Nat. Biotechnol."},{"key":"ref_124","doi-asserted-by":"crossref","first-page":"919","DOI":"10.1128\/JCM.03050-15","article-title":"Depletion of Human DNA in Spiked Clinical Specimens for Improvement of Sensitivity of Pathogen Detection by Next-Generation Sequencing","volume":"54","author":"Hasan","year":"2016","journal-title":"J. Clin. Microbiol."},{"key":"ref_125","doi-asserted-by":"crossref","unstructured":"Gan, M., Wu, B., Yan, G., Li, G., Sun, L., Lu, G., and Zhou, W. (2021). Combined nanopore adaptive sequencing and enzyme-based host depletion efficiently enriched microbial sequences and identified missing respiratory pathogens. BMC Genom., 22.","DOI":"10.1186\/s12864-021-08023-0"},{"key":"ref_126","doi-asserted-by":"crossref","first-page":"816","DOI":"10.1016\/j.tim.2023.02.008","article-title":"The challenges of defining the human nasopharyngeal resistome","volume":"31","author":"Heyderman","year":"2023","journal-title":"Trends Microbiol."},{"key":"ref_127","doi-asserted-by":"crossref","first-page":"688","DOI":"10.1038\/s41591-021-01289-7","article-title":"Integrative microbiomics in bronchiectasis exacerbations","volume":"27","author":"Narayana","year":"2021","journal-title":"Nat. Med."},{"key":"ref_128","doi-asserted-by":"crossref","first-page":"1277","DOI":"10.1586\/14787210.2014.952282","article-title":"Antimicrobial treatment of non-cystic fibrosis bronchiectasis","volume":"12","author":"Grimwood","year":"2014","journal-title":"Expert Rev. Anti-Infect. Ther."},{"key":"ref_129","doi-asserted-by":"crossref","first-page":"ofad425","DOI":"10.1093\/ofid\/ofad425","article-title":"The Utility of Metagenomic Next-Generation Sequencing (mNGS) in the Management of Patients With Bronchiectasis: A Single-Center Retrospective Study of 93 Cases","volume":"10","author":"Zhang","year":"2023","journal-title":"Open Forum Infect. Dis."},{"key":"ref_130","doi-asserted-by":"crossref","first-page":"274","DOI":"10.1016\/j.tibs.2017.01.004","article-title":"Metabolomics: A Primer","volume":"42","author":"Liu","year":"2017","journal-title":"Trends Biochem. Sci."},{"key":"ref_131","doi-asserted-by":"crossref","first-page":"034001","DOI":"10.1088\/1752-7163\/abf1d0","article-title":"A literature survey of all volatiles from healthy human breath and bodily fluids: The human volatilome","volume":"15","author":"Drabinska","year":"2021","journal-title":"J. Breath Res."},{"key":"ref_132","doi-asserted-by":"crossref","first-page":"3044","DOI":"10.1099\/mic.0.062687-0","article-title":"Characterization of volatile metabolites taken up by or released from Streptococcus pneumoniae and Haemophilus influenzae by using GC-MS","volume":"158","author":"Filipiak","year":"2012","journal-title":"Microbiology"},{"key":"ref_133","doi-asserted-by":"crossref","first-page":"208","DOI":"10.1016\/j.jchromb.2018.08.032","article-title":"The volatile molecular profiles of seven Streptococcus pneumoniae serotypes","volume":"1096","author":"Mellors","year":"2018","journal-title":"J. Chromatogr. B"},{"key":"ref_134","doi-asserted-by":"crossref","first-page":"1783","DOI":"10.1002\/bmc.3494","article-title":"Volatile organic compounds generated by cultures of bacteria and viruses associated with respiratory infections","volume":"29","author":"Lieberman","year":"2015","journal-title":"Biomed. Chromatogr."},{"key":"ref_135","doi-asserted-by":"crossref","first-page":"046014","DOI":"10.1088\/1752-7155\/10\/4\/046014","article-title":"Detection of Staphylococcus aureus in cystic fibrosis patients using breath VOC profiles","volume":"10","author":"Neerincx","year":"2016","journal-title":"J. Breath Res."},{"key":"ref_136","doi-asserted-by":"crossref","first-page":"026010","DOI":"10.1088\/1752-7155\/7\/2\/026010","article-title":"Hydrogen cyanide concentrations in the breath of adult cystic fibrosis patients with and without Pseudomonas aeruginosa infection","volume":"7","author":"Gilchrist","year":"2013","journal-title":"J. Breath Res."},{"key":"ref_137","doi-asserted-by":"crossref","first-page":"036013","DOI":"10.1088\/1752-7155\/10\/3\/036013","article-title":"Do linear logistic model analyses of volatile biomarkers in exhaled breath of cystic fibrosis patients reliably indicate Pseudomonas aeruginosa infection?","volume":"10","author":"Dryahina","year":"2016","journal-title":"J. Breath Res."},{"key":"ref_138","doi-asserted-by":"crossref","first-page":"610","DOI":"10.1111\/j.1472-765X.2011.03049.x","article-title":"Volatile biomarkers of Pseudomonas aeruginosa in cystic fibrosis and noncystic fibrosis bronchiectasis","volume":"52","author":"Savelev","year":"2011","journal-title":"Lett. Appl. Microbiol."},{"key":"ref_139","doi-asserted-by":"crossref","first-page":"826","DOI":"10.1038\/s41598-017-18491-8","article-title":"Volatile molecules from bronchoalveolar lavage fluid can \u2018rule-in\u2019 Pseudomonas aeruginosa and \u2018rule-out\u2019 Staphylococcus aureus infections in cystic fibrosis patients","volume":"8","author":"Nasir","year":"2018","journal-title":"Sci. Rep."},{"key":"ref_140","doi-asserted-by":"crossref","first-page":"102095","DOI":"10.1016\/j.pupt.2021.102095","article-title":"The immunomodulatory effects of macrolide antibiotics in respiratory disease","volume":"71","author":"Pollock","year":"2021","journal-title":"Pulm. Pharmacol. Ther."},{"key":"ref_141","doi-asserted-by":"crossref","first-page":"619","DOI":"10.1128\/AAC.27.4.619","article-title":"Tobramycin resistance of Pseudomonas aeruginosa cells growing as a biofilm on urinary catheter material","volume":"27","author":"Nickel","year":"1985","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_142","doi-asserted-by":"crossref","first-page":"ftw112","DOI":"10.1093\/femspd\/ftw112","article-title":"Resistance of non-typeable Haemophilus influenzae biofilms is independent of biofilm size","volume":"75","author":"Reimche","year":"2017","journal-title":"Pathog. Dis."},{"key":"ref_143","doi-asserted-by":"crossref","first-page":"67","DOI":"10.1159\/000320319","article-title":"Immunomodulatory effects of macrolide antibiotics\u2013part 1: Biological mechanisms","volume":"81","author":"Altenburg","year":"2010","journal-title":"Respiration"},{"key":"ref_144","doi-asserted-by":"crossref","first-page":"137","DOI":"10.1128\/AAC.00607-07","article-title":"Subinhibitory concentrations of azithromycin decrease nontypeable Haemophilus influenzae biofilm formation and diminish established biofilms","volume":"52","author":"Starner","year":"2008","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_145","doi-asserted-by":"crossref","first-page":"121","DOI":"10.1089\/jamp.2017.1415","article-title":"The rationale and evidence for use of inhaled antibiotics to control Pseudomonas aeruginosa infection in non-cystic fibrosis bronchiectasis","volume":"31","author":"Dhand","year":"2018","journal-title":"J. Aerosol Med. Pulm. Drug Deliv."},{"key":"ref_146","doi-asserted-by":"crossref","unstructured":"Cipolla, D., Blanchard, J., and Gonda, I. (2016). Development of liposomal ciprofloxacin to treat lung infections. Pharmaceutics, 8.","DOI":"10.3390\/pharmaceutics8010006"},{"key":"ref_147","doi-asserted-by":"crossref","first-page":"368","DOI":"10.1016\/j.ijpharm.2018.06.017","article-title":"A new therapeutic avenue for bronchiectasis: Dry powder inhaler of ciprofloxacin nanoplex exhibits superior ex vivo mucus permeability and antibacterial efficacy to its native ciprofloxacin counterpart","volume":"547","author":"Tran","year":"2018","journal-title":"Int. J. Pharm."},{"key":"ref_148","doi-asserted-by":"crossref","unstructured":"Tran, T.-T., and Hadinoto, K. (2020). Ternary nanoparticle complex of antibiotic, polyelectrolyte, and mucolytic enzyme as a potential antibiotic delivery system in bronchiectasis therapy. Colloids Surf. B Biointerfaces, 193.","DOI":"10.1016\/j.colsurfb.2020.111095"},{"key":"ref_149","doi-asserted-by":"crossref","first-page":"190","DOI":"10.1016\/j.rmed.2016.06.015","article-title":"The effect of N-acetylcysteine on biofilms: Implications for the treatment of respiratory tract infections","volume":"117","author":"Blasi","year":"2016","journal-title":"Respir. Med."},{"key":"ref_150","first-page":"4316","article-title":"Rationale and evidence for the adjunctive use of N-acetylcysteine in multidrug-resistant infections","volume":"27","author":"Oliva","year":"2023","journal-title":"Eur. Rev. Med. Pharmacol. Sci."},{"key":"ref_151","doi-asserted-by":"crossref","unstructured":"Tran, T.-T., and Hadinoto, K. (2021). A Potential Quorum-sensing inhibitor for bronchiectasis therapy: Quercetin\u2013chitosan nanoparticle complex exhibiting superior inhibition of biofilm formation and swimming motility of Pseudomonas aeruginosa to the native quercetin. Int. J. Mol. Sci., 22.","DOI":"10.3390\/ijms22041541"},{"key":"ref_152","doi-asserted-by":"crossref","first-page":"307","DOI":"10.1016\/j.freeradbiomed.2014.08.011","article-title":"Nitrite modulates bacterial antibiotic susceptibility and biofilm formation in association with airway epithelial cells","volume":"77","author":"Zemke","year":"2014","journal-title":"Free. Radic. Biol. Med."},{"key":"ref_153","doi-asserted-by":"crossref","first-page":"1329","DOI":"10.1378\/chest.113.5.1329","article-title":"Treatment of idiopathic bronchiectasis with aerosolized recombinant human DNase I","volume":"113","author":"Barker","year":"1998","journal-title":"Chest"},{"key":"ref_154","doi-asserted-by":"crossref","unstructured":"Goodman, S.D., and Bakaletz, L.O. (2022). Bacterial biofilms utilize an underlying extracellular DNA matrix structure that can be targeted for biofilm resolution. Microorganisms, 10.","DOI":"10.3390\/microorganisms10020466"},{"key":"ref_155","doi-asserted-by":"crossref","first-page":"1246","DOI":"10.1111\/mmi.12735","article-title":"Evaluation of the kinetics and mechanism of action of anti-integration host factor-mediated disruption of bacterial biofilms","volume":"93","author":"Brockson","year":"2014","journal-title":"Mol. Microbiol."},{"key":"ref_156","doi-asserted-by":"crossref","unstructured":"Mokrzan, E.M., Ahearn, C.P., Buzzo, J.R., Novotny, L.A., Zhang, Y., Goodman, S.D., and Bakaletz, L.O. (2020). Nontypeable Haemophilus influenzae newly released (NRel) from biofilms by antibody-mediated dispersal versus antibody-mediated disruption are phenotypically distinct. Biofilm, 2.","DOI":"10.1016\/j.bioflm.2020.100039"},{"key":"ref_157","doi-asserted-by":"crossref","first-page":"e02423-18","DOI":"10.1128\/mBio.02423-18","article-title":"Antibodies against the majority subunit (PilA) of the type IV pilus of nontypeable Haemophilus influenzae disperse Moraxella catarrhalis from a dual-species biofilm","volume":"9","author":"Mokrzan","year":"2018","journal-title":"mBio"},{"key":"ref_158","doi-asserted-by":"crossref","first-page":"192","DOI":"10.3109\/03009734.2014.902878","article-title":"Phage therapy\u2014Constraints and possibilities","volume":"119","author":"Nilsson","year":"2014","journal-title":"Upsala J. Med. Sci."},{"key":"ref_159","doi-asserted-by":"crossref","first-page":"525","DOI":"10.3390\/ph8030525","article-title":"Ecology of anti-biofilm agents I: Antibiotics versus bacteriophages","volume":"8","author":"Abedon","year":"2015","journal-title":"Pharmaceuticals"},{"key":"ref_160","doi-asserted-by":"crossref","first-page":"842","DOI":"10.1016\/j.ijantimicag.2018.09.006","article-title":"Bacteriophage Sb-1 enhances antibiotic activity against biofilm, degrades exopolysaccharide matrix and targets persisters of Staphylococcus aureus","volume":"52","author":"Tkhilaishvili","year":"2018","journal-title":"Int. J. Antimicrob. Agents"},{"key":"ref_161","doi-asserted-by":"crossref","first-page":"157","DOI":"10.1038\/s41564-020-00830-7","article-title":"Bacteriophage-resistant Acinetobacter baumannii are resensitized to antimicrobials","volume":"6","author":"Forsyth","year":"2021","journal-title":"Nat. Microbiol."},{"key":"ref_162","doi-asserted-by":"crossref","first-page":"e00066-18","DOI":"10.1128\/CMR.00066-18","article-title":"Phage therapy in the postantibiotic era","volume":"32","author":"Barr","year":"2019","journal-title":"Clin. Microbiol. Rev."},{"key":"ref_163","doi-asserted-by":"crossref","first-page":"349","DOI":"10.1111\/j.1749-4486.2009.01973.x","article-title":"A controlled clinical trial of a therapeutic bacteriophage preparation in chronic otitis due to antibiotic-resistant Pseudomonas aeruginosa; a preliminary report of efficacy","volume":"34","author":"Wright","year":"2009","journal-title":"Clin. Otolaryngol."},{"key":"ref_164","doi-asserted-by":"crossref","first-page":"104486","DOI":"10.1016\/j.jddst.2023.104486","article-title":"Inhalation phage therapy as a new approach to preventing secondary bacterial pneumonia in patients with moderate to severe COVID-19: A double-blind clinical trial study","volume":"84","author":"Samaee","year":"2023","journal-title":"J. Drug Deliv. Sci. Technol."},{"key":"ref_165","doi-asserted-by":"crossref","first-page":"1057","DOI":"10.1186\/s13063-022-07047-5","article-title":"Safety and microbiological activity of phage therapy in persons with cystic fibrosis colonized with Pseudomonas aeruginosa: Study protocol for a phase 1b\/2, multicenter, randomized, double-blind, placebo-controlled trial","volume":"23","author":"Tamma","year":"2022","journal-title":"Trials"},{"key":"ref_166","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1136\/thorax.57.1.15","article-title":"Bacterial colonisation in patients with bronchiectasis: Microbiological pattern and risk factors","volume":"57","author":"Angrill","year":"2002","journal-title":"Thorax"},{"key":"ref_167","doi-asserted-by":"crossref","first-page":"3629","DOI":"10.1038\/s41467-023-39370-z","article-title":"Personalized aerosolised bacteriophage treatment of a chronic lung infection due to multidrug-resistant Pseudomonas aeruginosa","volume":"14","author":"Luscher","year":"2023","journal-title":"Nat. Commun."},{"key":"ref_168","doi-asserted-by":"crossref","first-page":"4265","DOI":"10.2147\/IDR.S413900","article-title":"Refractory Pseudomonas aeruginosa Bronchopulmonary Infection After Lung Transplantation for Common Variable Immunodeficiency Despite Maximal Treatment Including IgM\/IgA-Enriched Immunoglobulins and Bacteriophage Therapy","volume":"16","author":"Cassir","year":"2023","journal-title":"Infect. Drug Resist."},{"key":"ref_169","doi-asserted-by":"crossref","first-page":"862","DOI":"10.1111\/1751-7915.14217","article-title":"First-in-human application of double-stranded RNA bacteriophage in the treatment of pulmonary Pseudomonas aeruginosa infection","volume":"16","author":"Li","year":"2023","journal-title":"Microb. Biotechnol."},{"key":"ref_170","doi-asserted-by":"crossref","unstructured":"Racenis, K., Lacis, J., Rezevska, D., Mukane, L., Vilde, A., Putnins, I., Djebara, S., Merabishvili, M., Pirnay, J.-P., and Kalnina, M. (2023). Successful Bacteriophage-Antibiotic Combination Therapy against Multidrug-Resistant Pseudomonas aeruginosa Left Ventricular Assist Device Driveline Infection. Viruses, 15.","DOI":"10.3390\/v15051210"},{"key":"ref_171","doi-asserted-by":"crossref","first-page":"1096","DOI":"10.1086\/651135","article-title":"Bacteriophages can treat and prevent Pseudomonas aeruginosa lung infections","volume":"201","author":"Debarbieux","year":"2010","journal-title":"J. Infect. Dis."},{"key":"ref_172","doi-asserted-by":"crossref","unstructured":"Le Guellec, S., Pardessus, J., Bodier-Montagutelli, E., L\u2019hostis, G., Dalloneau, E., Piel, D., Sama\u00ef, H.C., Guillon, A., Mujic, E., and Guillot-Combe, E. (2023). Administration of Bacteriophages via Nebulization during Mechanical Ventilation: In Vitro Study and Lung Deposition in Macaques. Viruses, 15.","DOI":"10.3390\/v15030602"},{"key":"ref_173","doi-asserted-by":"crossref","first-page":"e00472-23","DOI":"10.1128\/mbio.00472-23","article-title":"Engineered superinfective Pf phage prevents dissemination of Pseudomonas aeruginosa in a mouse burn model","volume":"14","author":"Prokopczuk","year":"2023","journal-title":"mBio"},{"key":"ref_174","doi-asserted-by":"crossref","first-page":"666","DOI":"10.1136\/thoraxjnl-2016-209265","article-title":"Phage therapy is highly effective against chronic lung infections with Pseudomonas aeruginosa","volume":"72","author":"Waters","year":"2017","journal-title":"Thorax"},{"key":"ref_175","doi-asserted-by":"crossref","first-page":"e00065-23","DOI":"10.1128\/iai.00065-23","article-title":"Class-Driven Synergy and Antagonism between a Pseudomonas Phage and Antibiotics","volume":"14","author":"Nicholls","year":"2023","journal-title":"Infect. Immun."},{"key":"ref_176","doi-asserted-by":"crossref","unstructured":"Martin, I., Morales, S., Alton, E.W., and Davies, J.C. (2023). Lytic Bacteriophage Is a Promising Adjunct to Common Antibiotics across Cystic Fibrosis Clinical Strains and Culture Models of Pseudomonas aeruginosa Infection. Antibiotics, 12.","DOI":"10.3390\/antibiotics12030593"},{"key":"ref_177","doi-asserted-by":"crossref","first-page":"103770","DOI":"10.1016\/j.micpath.2019.103770","article-title":"An experimental mouse model for phage therapy of bacterial pathogens causing bacteremia","volume":"137","author":"Kaabi","year":"2019","journal-title":"Microb. Pathog."},{"key":"ref_178","doi-asserted-by":"crossref","unstructured":"Abdelkader, K., Gerstmans, H., Saafan, A., Dishisha, T., and Briers, Y. (2019). The preclinical and clinical progress of bacteriophages and their lytic enzymes: The parts are easier than the whole. Viruses, 11.","DOI":"10.3390\/v11020096"},{"key":"ref_179","doi-asserted-by":"crossref","unstructured":"Iszatt, J.J., Larcombe, A.N., Chan, H.-K., Stick, S.M., Garratt, L.W., and Kicic, A. (2021). Phage therapy for multi-drug resistant respiratory tract infections. Viruses, 13.","DOI":"10.3390\/v13091809"},{"key":"ref_180","doi-asserted-by":"crossref","first-page":"e00029-23","DOI":"10.1128\/jb.00029-23","article-title":"F-Type Pyocins Are Diverse Noncontractile Phage Tail-Like Weapons for Killing Pseudomonas aeruginosa","volume":"205","author":"Saha","year":"2023","journal-title":"J. Bacteriol."},{"key":"ref_181","doi-asserted-by":"crossref","first-page":"156","DOI":"10.1016\/j.resmic.2019.01.003","article-title":"Protective and therapeutic application of the depolymerase derived from a novel KN1 genotype of Klebsiella pneumoniae bacteriophage in mice","volume":"170","author":"Wang","year":"2019","journal-title":"Res. Microbiol."},{"key":"ref_182","doi-asserted-by":"crossref","unstructured":"Liu, H., Hu, Z., Li, M., Yang, Y., Lu, S., and Rao, X. (2023). Therapeutic potential of bacteriophage endolysins for infections caused by Gram-positive bacteria. J. Biomed. Sci., 30.","DOI":"10.1186\/s12929-023-00919-1"},{"key":"ref_183","doi-asserted-by":"crossref","first-page":"6199","DOI":"10.1128\/IAI.71.11.6199-6204.2003","article-title":"Phage lytic enzyme Cpl-1 as a novel antimicrobial for pneumococcal bacteremia","volume":"71","author":"Loeffler","year":"2003","journal-title":"Infect. Immun."},{"key":"ref_184","doi-asserted-by":"crossref","first-page":"1215","DOI":"10.2217\/fmb-2018-0077","article-title":"Bactericidal synergism between antibiotics and phage endolysin Cpl-711 to kill multidrug-resistant pneumococcus","volume":"13","author":"Letrado","year":"2018","journal-title":"Future Microbiol."},{"key":"ref_185","doi-asserted-by":"crossref","first-page":"1159","DOI":"10.1093\/jac\/dkm342","article-title":"In vitro interactions of LytA, the major pneumococcal autolysin, with two bacteriophage lytic enzymes (Cpl-1 and Pal), cefotaxime and moxifloxacin against antibiotic-susceptible and-resistant Streptococcus pneumoniae strains","volume":"60","author":"Gracia","year":"2007","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_186","doi-asserted-by":"crossref","unstructured":"Guo, M., Feng, C., Ren, J., Zhuang, X., Zhang, Y., Zhu, Y., Dong, K., He, P., Guo, X., and Qin, J. (2017). A novel antimicrobial endolysin, LysPA26, against Pseudomonas aeruginosa. Front. Microbiol., 8.","DOI":"10.3389\/fmicb.2017.00293"},{"key":"ref_187","doi-asserted-by":"crossref","first-page":"3774","DOI":"10.1128\/AAC.02668-14","article-title":"Art-175 is a highly efficient antibacterial against multidrug-resistant strains and persisters of Pseudomonas aeruginosa","volume":"58","author":"Briers","year":"2014","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_188","doi-asserted-by":"crossref","unstructured":"Fauconnier, A. (2019). Phage therapy regulation: From night to dawn. Viruses, 11.","DOI":"10.3390\/v11040352"},{"key":"ref_189","doi-asserted-by":"crossref","first-page":"477","DOI":"10.1002\/ppul.10289","article-title":"Non-CF bronchiectasis: Clinical and HRCT evaluation","volume":"35","author":"Chang","year":"2003","journal-title":"Pediatr. Pulmonol."},{"key":"ref_190","doi-asserted-by":"crossref","first-page":"27","DOI":"10.3389\/fped.2017.00027","article-title":"The epidemiology of chronic suppurative lung disease and bronchiectasis in children and adolescents","volume":"5","author":"McCallum","year":"2017","journal-title":"Front. Pediatr."},{"key":"ref_191","doi-asserted-by":"crossref","first-page":"189","DOI":"10.1002\/ppul.22763","article-title":"Indigenous children from three countries with non-cystic fibrosis chronic suppurative lung disease\/bronchiectasis","volume":"49","author":"Singleton","year":"2014","journal-title":"Pediatr. Pulmonol."},{"key":"ref_192","doi-asserted-by":"crossref","first-page":"182","DOI":"10.1002\/(SICI)1099-0496(200003)29:3<182::AID-PPUL5>3.0.CO;2-T","article-title":"Bronchiectasis in Alaska Native children: Causes and clinical courses","volume":"29","author":"Singleton","year":"2000","journal-title":"Pediatr. Pulmonol."},{"key":"ref_193","doi-asserted-by":"crossref","first-page":"96","DOI":"10.1513\/AnnalsATS.201406-257OC","article-title":"Bronchiectasis in children from Qikiqtani (Baffin) Region, Nunavut, Canada","volume":"12","author":"Das","year":"2015","journal-title":"Ann. Am. Thorac. Soc."},{"key":"ref_194","doi-asserted-by":"crossref","first-page":"111","DOI":"10.3389\/fped.2017.00111","article-title":"Early-Life Host-Microbiome Interphase: The Key Frontier for Immune Development","volume":"5","author":"Amenyogbe","year":"2017","journal-title":"Front. Pediatr."},{"key":"ref_195","doi-asserted-by":"crossref","first-page":"e00036-17","DOI":"10.1128\/MMBR.00036-17","article-title":"The First Microbial Colonizers of the Human Gut: Composition, Activities, and Health Implications of the Infant Gut Microbiota","volume":"81","author":"Milani","year":"2017","journal-title":"Microbiol. Mol. Biol. Rev."},{"key":"ref_196","doi-asserted-by":"crossref","first-page":"443","DOI":"10.1038\/s41467-020-20495-4","article-title":"Neonatal antibiotic exposure impairs child growth during the first six years of life by perturbing intestinal microbial colonization","volume":"12","author":"Turta","year":"2021","journal-title":"Nat. Commun."},{"key":"ref_197","doi-asserted-by":"crossref","unstructured":"Hill, C.J., Lynch, D.B., Murphy, K., Ulaszewska, M., Jeffery, I.B., O\u2019Shea, C.A., Watkins, C., Dempsey, E., Mattivi, F., and Tuohy, K. (2017). Evolution of gut microbiota composition from birth to 24 weeks in the INFANTMET Cohort. Microbiome, 5.","DOI":"10.1186\/s40168-016-0213-y"},{"key":"ref_198","doi-asserted-by":"crossref","first-page":"713","DOI":"10.1038\/nm.4142","article-title":"The microbiome in early life: Implications for health outcomes","volume":"22","author":"Tamburini","year":"2016","journal-title":"Nat. Med."},{"key":"ref_199","doi-asserted-by":"crossref","first-page":"222","DOI":"10.1038\/nature11053","article-title":"Human gut microbiome viewed across age and geography","volume":"486","author":"Yatsunenko","year":"2012","journal-title":"Nature"},{"key":"ref_200","doi-asserted-by":"crossref","first-page":"115","DOI":"10.1159\/000496426","article-title":"Beneficial Effects of Probiotic Consumption on the Immune System","volume":"74","author":"Cazorla","year":"2019","journal-title":"Ann. Nutr. Metab."},{"key":"ref_201","doi-asserted-by":"crossref","first-page":"341","DOI":"10.1038\/nri.2016.42","article-title":"Gut microbiota, metabolites and host immunity","volume":"16","author":"Rooks","year":"2016","journal-title":"Nat. Rev. Immunol."},{"key":"ref_202","doi-asserted-by":"crossref","first-page":"307ra152","DOI":"10.1126\/scitranslmed.aab2271","article-title":"Early infancy microbial and metabolic alterations affect risk of childhood asthma","volume":"7","author":"Arrieta","year":"2015","journal-title":"Sci. Transl. Med."},{"key":"ref_203","doi-asserted-by":"crossref","first-page":"979","DOI":"10.1093\/advances\/nmaa003","article-title":"Preventing Respiratory Tract Infections by Synbiotic Interventions: A Systematic Review and Meta-Analysis of Randomized Controlled Trials","volume":"11","author":"Chan","year":"2020","journal-title":"Adv. Nutr."},{"key":"ref_204","first-page":"CD006895","article-title":"Probiotics for preventing acute upper respiratory tract infections","volume":"8","author":"Hao","year":"2015","journal-title":"Cochrane Database Syst. Rev."},{"key":"ref_205","doi-asserted-by":"crossref","first-page":"8","DOI":"10.1542\/peds.2007-1192","article-title":"Long-term safety and impact on infection rates of postnatal probiotic and prebiotic (synbiotic) treatment: Randomized, double-blind, placebo-controlled trial","volume":"122","author":"Kukkonen","year":"2008","journal-title":"Pediatrics"},{"key":"ref_206","doi-asserted-by":"crossref","first-page":"405","DOI":"10.1016\/j.jaci.2013.08.020","article-title":"Prebiotic and probiotic supplementation prevents rhinovirus infections in preterm infants: A randomized, placebo-controlled trial","volume":"133","author":"Luoto","year":"2014","journal-title":"J. Allergy Clin. Immunol."},{"key":"ref_207","doi-asserted-by":"crossref","first-page":"407","DOI":"10.1038\/nature23480","article-title":"A randomized synbiotic trial to prevent sepsis among infants in rural India","volume":"548","author":"Panigrahi","year":"2017","journal-title":"Nature"},{"key":"ref_208","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.nut.2006.09.007","article-title":"Clinical evaluation of a new starter formula for infants containing live Bifidobacterium longum BL999 and prebiotics","volume":"23","author":"Puccio","year":"2007","journal-title":"Nutrition"},{"key":"ref_209","doi-asserted-by":"crossref","first-page":"1722","DOI":"10.1017\/S0007114508116282","article-title":"Specific probiotics in reducing the risk of acute infections in infancy\u2014A randomised, double-blind, placebo-controlled study","volume":"101","author":"Rautava","year":"2009","journal-title":"Br. J. Nutr."},{"key":"ref_210","doi-asserted-by":"crossref","first-page":"409","DOI":"10.1017\/S0007114510003685","article-title":"Bifidobacterium animalis subsp. lactis BB-12 in reducing the risk of infections in infancy","volume":"105","author":"Taipale","year":"2011","journal-title":"Br. J. Nutr."},{"key":"ref_211","doi-asserted-by":"crossref","first-page":"65","DOI":"10.1038\/pr.2015.174","article-title":"Bifidobacterium animalis subsp. lactis BB-12 in reducing the risk of infections in early childhood","volume":"79","author":"Taipale","year":"2016","journal-title":"Pediatr. Res."},{"key":"ref_212","doi-asserted-by":"crossref","unstructured":"Segal, L.N., Clemente, J.C., Tsay, J.C., Koralov, S.B., Keller, B.C., Wu, B.G., Li, Y., Shen, N., Ghedin, E., and Morris, A. (2016). Enrichment of the lung microbiome with oral taxa is associated with lung inflammation of a Th17 phenotype. Nat. Microbiol., 1.","DOI":"10.1038\/nmicrobiol.2016.31"},{"key":"ref_213","doi-asserted-by":"crossref","first-page":"1099","DOI":"10.1164\/rccm.202005-1596OC","article-title":"Episodic Aspiration with Oral Commensals Induces a MyD88-dependent, Pulmonary T-Helper Cell Type 17 Response that Mitigates Susceptibility to Streptococcus pneumoniae","volume":"203","author":"Wu","year":"2021","journal-title":"Am. J. Respir. Crit. Care Med."},{"key":"ref_214","doi-asserted-by":"crossref","first-page":"1582","DOI":"10.1164\/rccm.201703-0554OC","article-title":"Maturation of the Infant Respiratory Microbiota, Environmental Drivers, and Health Consequences. A Prospective Cohort Study","volume":"196","author":"Bosch","year":"2017","journal-title":"Am. J. Respir. Crit. Care Med."},{"key":"ref_215","doi-asserted-by":"crossref","first-page":"9949","DOI":"10.1007\/s00253-018-9403-9","article-title":"Immunobiosis and probiosis: Antimicrobial activity of lactic acid bacteria with a focus on their antiviral and antifungal properties","volume":"102","author":"Arena","year":"2018","journal-title":"Appl. Microbiol. Biotechnol."},{"key":"ref_216","doi-asserted-by":"crossref","unstructured":"Wang, Z., Chai, W., Burwinkel, M., Twardziok, S., Wrede, P., Palissa, C., Esch, B., and Schmidt, M.F.G. (2013). Inhibitory Influence of Enterococcus faecium on the Propagation of Swine Influenza A Virus In Vitro. PLoS ONE, 8.","DOI":"10.1371\/journal.pone.0053043"},{"key":"ref_217","doi-asserted-by":"crossref","unstructured":"Gao, X., Huang, L., Zhu, L., Mou, C., Hou, Q., and Yu, Q. (2016). Inhibition of H9N2 Virus Invasion into Dendritic Cells by the S-Layer Protein from L. acidophilus ATCC 4356. Front. Cell. Infect. Microbiol., 6.","DOI":"10.3389\/fcimb.2016.00137"},{"key":"ref_218","doi-asserted-by":"crossref","first-page":"177","DOI":"10.1007\/s12602-014-9162-6","article-title":"Antiviral Potential of Lactic Acid Bacteria and Their Bacteriocins","volume":"6","author":"Hober","year":"2014","journal-title":"Probiotics Antimicrob. Proteins"},{"key":"ref_219","doi-asserted-by":"crossref","first-page":"951","DOI":"10.2217\/fvl.11.63","article-title":"Influenza-induced innate immunity: Regulators of viral replication, respiratory tract pathology & adaptive immunity","volume":"6","author":"Oslund","year":"2011","journal-title":"Future Virol."},{"key":"ref_220","doi-asserted-by":"crossref","first-page":"270","DOI":"10.1016\/j.antiviral.2012.12.022","article-title":"Lactobacillus priming of the respiratory tract: Heterologous immunity and protection against lethal pneumovirus infection","volume":"97","author":"Chan","year":"2013","journal-title":"Antivir. Res."},{"key":"ref_221","doi-asserted-by":"crossref","first-page":"948","DOI":"10.3389\/fimmu.2017.00948","article-title":"Peptidoglycan from Immunobiotic Lactobacillus rhamnosus Improves Resistance of Infant Mice to Respiratory Syncytial Viral Infection and Secondary Pneumococcal Pneumonia","volume":"8","author":"Clua","year":"2017","journal-title":"Front. Immunol."},{"key":"ref_222","doi-asserted-by":"crossref","unstructured":"Groeger, D., Schiavi, E., Grant, R., Kurnik-\u0141ucka, M., Michalovich, D., Williamson, R., Beinke, S., Kiely, B., Akdis, C.A., and Hessel, E.M. (2020). Intranasal Bifidobacterium longum protects against viral-induced lung inflammation and injury in a murine model of lethal influenza infection. EBioMedicine, 60.","DOI":"10.1016\/j.ebiom.2020.102981"},{"key":"ref_223","doi-asserted-by":"crossref","unstructured":"Atto, B., Kunde, D., Gell, D.A., and Tristram, S. (2021). Oropharyngeal Carriage of hpl-Containing Haemophilus haemolyticus Predicts Lower Prevalence and Density of NTHi Colonisation in Healthy Adults. Pathogens, 10.","DOI":"10.3390\/pathogens10050577"},{"key":"ref_224","doi-asserted-by":"crossref","first-page":"1641","DOI":"10.21037\/jtd-20-1662","article-title":"Effect of OM-85 BV on reducing bronchiectasis exacerbation in Chinese patients: The iPROBE study","volume":"13","author":"Gao","year":"2021","journal-title":"J. Thorac. Dis."},{"key":"ref_225","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1016\/j.ccm.2021.11.002","article-title":"Microbiology and the Microbiome in Bronchiectasis","volume":"43","author":"Chotirmall","year":"2022","journal-title":"Clin. Chest Med."},{"key":"ref_226","doi-asserted-by":"crossref","unstructured":"Earl, J.P., Adappa, N.D., Krol, J., Bhat, A.S., Balashov, S., Ehrlich, R.L., Palmer, J.N., Workman, A.D., Blasetti, M., and Sen, B. (2018). Species-level bacterial community profiling of the healthy sinonasal microbiome using Pacific Biosciences sequencing of full-length 16S rRNA genes. Microbiome, 6.","DOI":"10.1186\/s40168-018-0569-2"}],"container-title":["Journal of Clinical Medicine"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2077-0383\/13\/1\/171\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T21:43:09Z","timestamp":1760132589000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2077-0383\/13\/1\/171"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,12,28]]},"references-count":226,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2024,1]]}},"alternative-id":["jcm13010171"],"URL":"https:\/\/doi.org\/10.3390\/jcm13010171","relation":{},"ISSN":["2077-0383"],"issn-type":[{"value":"2077-0383","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,12,28]]}}}